Chapter 10 Differential abundance analysis: functional

load("data/data.Rdata")

List of 11
 $ axis.title      :List of 11
  ..$ family       : NULL
  ..$ face         : chr "bold"
  ..$ colour       : NULL
  ..$ size         : num 12
  ..$ hjust        : NULL
  ..$ vjust        : NULL
  ..$ angle        : NULL
  ..$ lineheight   : NULL
  ..$ margin       : NULL
  ..$ debug        : NULL
  ..$ inherit.blank: logi FALSE
  ..- attr(*, "class")= chr [1:2] "element_text" "element"
 $ axis.title.x    :List of 11
  ..$ family       : NULL
  ..$ face         : NULL
  ..$ colour       : NULL
  ..$ size         : NULL
  ..$ hjust        : NULL
  ..$ vjust        : NULL
  ..$ angle        : NULL
  ..$ lineheight   : NULL
  ..$ margin       : 'margin' num [1:4] 20points 0points 0points 0points
  .. ..- attr(*, "unit")= int 8
  ..$ debug        : NULL
  ..$ inherit.blank: logi FALSE
  ..- attr(*, "class")= chr [1:2] "element_text" "element"
 $ axis.title.y    :List of 11
  ..$ family       : NULL
  ..$ face         : NULL
  ..$ colour       : NULL
  ..$ size         : NULL
  ..$ hjust        : NULL
  ..$ vjust        : NULL
  ..$ angle        : NULL
  ..$ lineheight   : NULL
  ..$ margin       : 'margin' num [1:4] 0points 20points 0points 0points
  .. ..- attr(*, "unit")= int 8
  ..$ debug        : NULL
  ..$ inherit.blank: logi FALSE
  ..- attr(*, "class")= chr [1:2] "element_text" "element"
 $ axis.text.x     :List of 11
  ..$ family       : NULL
  ..$ face         : NULL
  ..$ colour       : NULL
  ..$ size         : num 6
  ..$ hjust        : num 1
  ..$ vjust        : num 0.5
  ..$ angle        : num 90
  ..$ lineheight   : NULL
  ..$ margin       : NULL
  ..$ debug        : NULL
  ..$ inherit.blank: logi FALSE
  ..- attr(*, "class")= chr [1:2] "element_text" "element"
 $ axis.text.y     :List of 11
  ..$ family       : NULL
  ..$ face         : NULL
  ..$ colour       : NULL
  ..$ size         : NULL
  ..$ hjust        : NULL
  ..$ vjust        : NULL
  ..$ angle        : NULL
  ..$ lineheight   : NULL
  ..$ margin       : NULL
  ..$ debug        : NULL
  ..$ inherit.blank: logi FALSE
  ..- attr(*, "class")= chr [1:2] "element_text" "element"
 $ panel.background: list()
  ..- attr(*, "class")= chr [1:2] "element_blank" "element"
 $ strip.background: list()
  ..- attr(*, "class")= chr [1:2] "element_blank" "element"
 $ strip.text      :List of 11
  ..$ family       : NULL
  ..$ face         : NULL
  ..$ colour       : chr "black"
  ..$ size         : num 10
  ..$ hjust        : NULL
  ..$ vjust        : NULL
  ..$ angle        : NULL
  ..$ lineheight   : NULL
  ..$ margin       : NULL
  ..$ debug        : NULL
  ..$ inherit.blank: logi FALSE
  ..- attr(*, "class")= chr [1:2] "element_text" "element"
 $ y               : chr "Traits"
 $ x               : chr "Samples"
 $ fill            : chr "GIFT"
 - attr(*, "class")= chr [1:2] "theme" "gg"
 - attr(*, "complete")= logi FALSE
 - attr(*, "validate")= logi TRUE

10.1 Wilcoxon

10.1.1 Community elements differences:

   Elements     Daneborg Ittoqqortoormii                                        Function
1     B0103 4.803665e-01    0.5691376000               Nucleic acid biosynthesis_UDP/UTP
2     B0205 3.986630e-01    0.3628119000               Amino acid biosynthesis_Threonine
3     B0207 3.776322e-01    0.4098170000              Amino acid biosynthesis_Methionine
4     B0213 5.541612e-01    0.5034503000                 Amino acid biosynthesis_Proline
5     B0219 2.331814e-03    0.0041099320                    Amino acid biosynthesis_GABA
6     B0220 8.256612e-02    0.0708564200            Amino acid biosynthesis_Beta-alanine
7     B0221 1.846192e-01    0.2143759000               Amino acid biosynthesis_Ornithine
8     B0307 2.212079e-01    0.2715057000   Amino acid derivative biosynthesis_Spermidine
9     B0702 5.196989e-01    0.4704878000            Vitamin biosynthesis_Riboflavin (B2)
10    B0704 2.289657e-01    0.2619218000          Vitamin biosynthesis_Pantothenate (B5)
11    B0705 2.685152e-01    0.2187839000           Vitamin biosynthesis_Pyridoxal-P (B6)
12    B0708 2.866538e-01    0.3360235000            Vitamin biosynthesis_Cobalamin (B12)
13    B0710 4.007905e-02    0.0475397500         Vitamin biosynthesis_Phylloquinone (K1)
14    B0801 1.539881e-03    0.0021263090       Aromatic compound biosynthesis_Salicylate
15    B0802 3.886593e-01    0.4737292000          Aromatic compound biosynthesis_Gallate
16    B0805 1.164352e-01    0.1026751000 Aromatic compound biosynthesis_Indole-3-acetate
17    B0902 1.030715e-03    0.0001853436            Metallophore biosynthesis_Aerobactin
18    B1012 6.541175e-03    0.0040366720              Antibiotic biosynthesis_Fosfomycin
19    B1028 4.633777e-03    0.0084958210               Antibiotic biosynthesis_Pyocyanin
20    D0102 7.090557e-02    0.0612379700                    Lipid degradation_Fatty acid
21    D0103 6.328203e-02    0.0514885300                        Lipid degradation_Oleate
22    D0201 1.448753e-01    0.1295450000            Polysaccharide degradation_Cellulose
23    D0203 2.786198e-01    0.2977752000               Polysaccharide degradation_Starch
24    D0205 8.817280e-02    0.0988987600               Polysaccharide degradation_Pectin
25    D0206 2.637350e-01    0.3466158000       Polysaccharide degradation_Alpha galactan
26    D0207 3.824963e-01    0.4391534000        Polysaccharide degradation_Beta-galactan
27    D0211 4.875337e-02    0.0622591200         Polysaccharide degradation_Alpha-mannan
28    D0213 1.573168e-01    0.2121044000                Polysaccharide degradation_Mucin
29    D0302 7.282498e-02    0.1039446400                       Sugar degradation_Sucrose
30    D0304 1.320346e-01    0.1580921000                   Sugar degradation_D-Arabinose
31    D0305 3.526289e-01    0.3060427000                     Sugar degradation_D-Mannose
32    D0306 7.155777e-02    0.0854695200                      Sugar degradation_D-Xylose
33    D0307 1.504186e-01    0.1774106000                      Sugar degradation_L-Fucose
34    D0309 3.691148e-01    0.4352184000                     Sugar degradation_Galactose
35    D0310 2.138309e-01    0.2382948000                         Sugar degradation_NeuAc
36    D0501 7.120569e-01    0.7568889000                   Amino acid degradation_Serine
37    D0503 1.647386e-02    0.0225366200                 Amino acid degradation_Cysteine
38    D0504 8.992973e-02    0.0667828400               Amino acid degradation_Methionine
39    D0509 3.249079e-01    0.3824282000                 Amino acid degradation_Arginine
40    D0511 4.687518e-01    0.4222418000                Amino acid degradation_Glutamate
41    D0516 3.849915e-03    0.0034554200             Amino acid degradation_Beta-alanine
42    D0603 2.165105e-03    0.0023180440             Nitrogen compound degradation_Urate
43    D0604 4.308410e-01    0.5173848000            Nitrogen compound degradation_GlcNAc
44    D0608 1.869179e-04    0.0005024345           Nitrogen compound degradation_Betaine
45    D0609 1.259039e-01    0.1087170000       Nitrogen compound degradation_L-carnitine
46    D0613 3.450657e-01    0.3032557000           Nitrogen compound degradation_Taurine
47    D0701 6.462446e-04    0.0090044261              Alcohol degradation_2,3-Butanediol
48    D0704 6.122587e-01    0.5540933000                    Alcohol degradation_Glycerol
49    D0705 2.590039e-01    0.2895818000            Alcohol degradation_Propylene glycol
50    D0708 1.296890e-01    0.1121187000                      Alcohol degradation_Phytol
51    D0801 2.013642e-05    0.0005815505                  Xenobiotic degradation_Toluene
52    D0802 2.013642e-05    0.0005815505                   Xenobiotic degradation_Xylene
53    D0805 6.101943e-05    0.0017622740                 Xenobiotic degradation_Benzoate
54    D0807 8.328293e-03    0.0134305770                 Xenobiotic degradation_Catechol
55    D0817 7.141985e-03    0.0071624840          Xenobiotic degradation_Trans-cinnamate
56    D0902 2.005745e-02    0.0059254260               Antibiotic degradation_Carbapenem
57    D0903 4.717263e-03    0.0057007140            Antibiotic degradation_Cephalosporin
58    D0905 8.576596e-02    0.1601438000            Antibiotic degradation_Streptogramin
59    D0911 1.398233e-01    0.2053753000              Antibiotic degradation_Lincosamide
60    S0101 7.166048e-01    0.6934966000                Cellular structure_Peptidoglycan
61    S0104 1.371278e-01    0.1821940000            Cellular structure_Lipoteichoic acid
62    S0201 1.839605e-01    0.2757946000                            Appendages_Flagellum

10.1.2 Community functions differences

  Code_function   Daneborg Ittoqqortoormii                           Function
1           B03 0.08046173       0.0915978 Amino acid derivative biosynthesis
2           D02 0.19474800       0.2156341         Polysaccharide degradation
3           D07 0.37611120       0.3482431                Alcohol degradation
4           D09 0.14213640       0.1582357             Antibiotic degradation
5           S02 0.07926413       0.1203754                         Appendages

10.1.3 Community domains differences

No differences

10.2 Ancombc2

10.2.1 Element level

ancombc_rand_table <- ancom_rand_output_element$res %>%
  dplyr::select(taxon, lfc_regionIttoqqortoormii, p_regionIttoqqortoormii) %>%
  filter(p_regionIttoqqortoormii < 0.05) %>%
  dplyr::arrange(p_regionIttoqqortoormii) %>%
  merge(., tax, by="taxon")

10.2.2 Functional level

ancombc_rand_table_func <- ancom_rand_output_function$res %>%
  dplyr::select(taxon, lfc_regionIttoqqortoormii, p_regionIttoqqortoormii) %>%
  filter(p_regionIttoqqortoormii < 0.05) %>%
  dplyr::arrange(p_regionIttoqqortoormii) %>%
  merge(., tax, by="taxon")